Palmer penguins PCA

Reading in data

Penguins data…

## # A tibble: 344 x 8
##    species island    bill_length_mm bill_depth_mm flipper_length_mm body_mass_g
##    <fct>   <fct>              <dbl>         <dbl>             <int>       <int>
##  1 Adelie  Torgersen           39.1          18.7               181        3750
##  2 Adelie  Torgersen           39.5          17.4               186        3800
##  3 Adelie  Torgersen           40.3          18                 195        3250
##  4 Adelie  Torgersen           NA            NA                  NA          NA
##  5 Adelie  Torgersen           36.7          19.3               193        3450
##  6 Adelie  Torgersen           39.3          20.6               190        3650
##  7 Adelie  Torgersen           38.9          17.8               181        3625
##  8 Adelie  Torgersen           39.2          19.6               195        4675
##  9 Adelie  Torgersen           34.1          18.1               193        3475
## 10 Adelie  Torgersen           42            20.2               190        4250
## # ... with 334 more rows, and 2 more variables: sex <fct>, year <int>

How do they differ?

Data processing

PCA recipe

Apply the PCA

## # A tibble: 333 x 6
##    species    PC1     PC2     PC3    PC4     PC5
##    <fct>    <dbl>   <dbl>   <dbl>  <dbl>   <dbl>
##  1 Adelie  -1.82  -0.596   0.965   0.322 -0.879 
##  2 Adelie  -1.37   0.313   0.456   0.228 -0.707 
##  3 Adelie  -1.43   0.115   0.192   0.114 -0.838 
##  4 Adelie  -1.93  -0.0408  0.813  -0.247 -0.462 
##  5 Adelie  -1.89  -1.22    1.09   -0.279 -0.693 
##  6 Adelie  -1.82   0.258   0.415   0.181 -0.743 
##  7 Adelie  -0.797 -1.02    1.64   -0.229 -0.351 
##  8 Adelie  -1.85   0.199  -0.0902  0.290 -1.04  
##  9 Adelie  -1.92  -1.38    1.31   -0.486 -0.537 
## 10 Adelie  -1.53  -1.11    2.19   -0.545 -0.0420
## # ... with 323 more rows

This is what the output looks like

What are the components made of?

Plotting the different components

Easy to separate the Gentoos. More difficult to seperate the Adelie and Chinstrap

Using PCA1 and PCA3 it is easy to seperate the different species.

3D plot

We can even make a nice plot in 3-dimensions. You can zoom in and look around with your mouse.